RetrogeneDB ID: retro_pabe_2109

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 2b:29812201..29812746(-)
• Located in intron of: ENSPPYG00000012826

Retrocopy information

• Ensembl ID: None
• Aliases: None
• Status: NOVEL

Parental gene information

• Parental gene symbol: COPRS
• Ensembl ID: ENSPPYG00000008153
• Aliases: None
• Description: coordinator of PRMT5, differentiation stimulator [Source:HGNC Symbol;Acc:28848]

Sequence

>retro_pabe_2109
ATGGACCCTCAGTCCGCCAGGGCCCAGGCGCAGGGGGCCGCGGAGCTGTTTCGGGGCCCGCTGCTGCCTAGCGCGTGGAA
GGCACCCCCTAGCCCGGAGGCTGGCTTTGCTACAGCGGGCCACTCCTGTCAGGAGAGAGAGACTGAGAAGGCTATGGATC
GACTAGCCCGGGGAGCACAGAGCGTCTCTAATGACAGTCGAGCCCGGGGTGAGGGCACCCATTCTGAAGAGGAAGGATTT
GCTGTGAATGCGGAGGACTCTGATGGAATACCTGGGAGCTGAGAGAAGGGACAAACTGTCCACCCAAGGAACAGCCTGGC
AATCTTTTTAATGAAGACTGGGACTTGGAGTTGAAAGCAGATCAAGGGAATCCGTATGAGGCTGACGACATCCAGGGGAG
CATTTCTCAAGATCTCAAACCTTGGGTCAGCTGTGCCCCATAAGGAGACATGATCTATGACCCCAGGTGGCACCATCCAC
CTCAACTGATAACCCATTATTCCAAGATGGTCTTTGAAACAGGATAGTTTGACGATGCCAAAGAT

Alignment

ORF - retro_pabe_2109 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 73.51 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 2
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MDLQAAGAQAQGAAEPSRGPPLPSARGAPPSPEAGFATADHSGQERKTEKAMDRLARGAQSIPNDSPARG
          MD.Q.A.AQAQGAAE..RGP.LPSA..APPSPEAGFATA.HS.QER.TEKAMDRLARGAQS..ND...R.
Retrocopy MDPQSARAQAQGAAELFRGPLLPSAWKAPPSPEAGFATAGHSCQERETEKAMDRLARGAQSVSND--SRA

Parental  EGTHSEEEGFAMDEEDSDGE-LNTWELSEGTNCPPKEQPGDLFNEDWDLELKADQGNPYDADDIQESISQ
          .G.....E.........D....NTWEL.EGTNCPPKEQPG.LFNEDWDLELKADQGNPY.ADDIQ.SISQ
Retrocopy RGEGTHSEEEGFAVNAEDSD<WNTWELREGTNCPPKEQPGNLFNEDWDLELKADQGNPYEADDIQGSISQ

Parental  ELKPWVCCAPQGDMIYDPSWHHPPPLIPYYSKMVFETGQFDDAED
          .LKPWV.CAP.GDMIYDP.WHHPP.LI..YSKMVFETG.FDDA.D
Retrocopy DLKPWVSCAP*GDMIYDPRWHHPPQLITHYSKMVFETG*FDDAKD

Legend:

• *: Stop codon
• >: Forward frameshift by one nucleotide
• <: Reverse frameshift by one nucleotide

Expression

RNA-Seq

Expression validation based on RNA-Seq data:

Library	Retrocopy expression	Parental gene expression
SRP007412_brain_prefrontal_cortex	0.00 RPM	41.36 RPM
SRP007412_cerebellum	0.00 RPM	24.08 RPM
SRP007412_heart	0.00 RPM	10.05 RPM
SRP007412_kidney	0.03 RPM	15.78 RPM
SRP007412_liver	0.00 RPM	10.74 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_2109 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_2109 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_2109 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 7 parental genes, and 7 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000001885	1 retrocopy	retro_btau_946,
Callithrix jacchus	ENSCJAG00000014110	1 retrocopy	retro_cjac_2739,
Myotis lucifugus	ENSMLUG00000016418	1 retrocopy	retro_mluc_1801,
Pongo abelii	ENSPPYG00000008153	1 retrocopy	retro_pabe_2109 ,
Rattus norvegicus	ENSRNOG00000000111	1 retrocopy	retro_rnor_2923,
Tupaia belangeri	ENSTBEG00000008542	1 retrocopy	retro_tbel_1528,
Tursiops truncatus	ENSTTRG00000009909	1 retrocopy	retro_ttru_225,